Why is the output file in FASTA format?

[MGI-tech-bioinformatics]

Why is the output file in FASTA format? According to the flowchart introduction in the literature (https://doi.org/10.1038/s42003-024-07376-y), the final output file of dechat is the corrected reads, and reads are usually saved in FASTQ format, right?

[Yichen-HNU]

Hi,

For error correction, the corrected bases are no longer correlated with their sequence quality at the time of sequencing, especially for indels errors, it is not possible to correlate the corresponding sequence quality to match, so for most error correction tools, the output is more in FASTA than FASTQ format, dechat belongs to this category.

[MGI-tech-bioinformatics]

Hi,

For error correction, the corrected bases are no longer correlated with their sequence quality at the time of sequencing, especially for indels errors, it is not possible to correlate the corresponding sequence quality to match, so for most error correction tools, the output is more in FASTA than FASTQ format, dechat belongs to this category.

However, if we want to use the corrected reads for further analysis, the software can only read them in FASTQ format. How can we solve this problem?

[alexpmagalhaes]

Hi,
For error correction, the corrected bases are no longer correlated with their sequence quality at the time of sequencing, especially for indels errors, it is not possible to correlate the corresponding sequence quality to match, so for most error correction tools, the output is more in FASTA than FASTQ format, dechat belongs to this category.

However, if we want to use the corrected reads for further analysis, the software can only read them in FASTQ format. How can we solve this problem?

If you want this you can use awk to insert quality scores in the proper lines.

assuming that you want Sanger formated fastq with Phred+33 encoding you can:

awk 'BEGIN {RS = ">" ; FS = "\n"} NR > 1 {print "@"$1"\n"$2"\n+"; for(c=0;c<length($2);c++) printf "j"; printf "\n"}' yourfastafile.fa > yourfastafile.fq

Remember that garbage in > garbage out